The recent development of the intense pulsed muon source at J-PARC MUSE, Japan Proton Accelerator Research Complex/MUon Science Establishment (106 s−1 for a momentum of 60 MeV/c), enabled us to pioneer a new frontier in analytical sciences. Here, we report a non-destructive elemental analysis using µ− capture. Controlling muon momentum from 32.5 to 57.5 MeV/c, we successfully demonstrate a depth-profile analysis of light elements (B, C, N, and O) from several mm-thick layered materials and non-destructive bulk analyses of meteorites containing organic materials. Muon beam analysis, enabling a bulk analysis of light to heavy elements without severe radioactivation, is a unique analytical method complementary to other non-destructive analyses. Furthermore, this technology can be used as a powerful tool to identify the content and distribution of organic components in future asteroidal return samples.